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Printing them out in a different orientation seemed to help a little bit but the real problem was that the printer was not perfectly square. That is what the SquareCal was meant to test. Heating up an assembled chain and gently encouraging it to straighten out is a good idea. If your 3d printer is perfectly square, or in the case of a delta printer - set up perfectly, then the assembled chain should be perfectly straight. The MakerBot Thing-O-Matic that I used when creating these was noticeably NOT square and there was nothing that could be done about it. The laser cut parts that the TOM was built out of were very, very slightly out of square and that translated to the 3d prints also being slightly out of square.